Isolation and Quantification of Uremic Toxin Precursor-Generating Gut
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Supplementary Tables and Figures
SUPPLEMENTARY TABLES AND FIGURES Table S1: Isolated microorganisms from three fecal samples from controls on five different media. YCFAG SCH Δ0 ΔV ΔS SCH SCH +AAA +FS +AAA +FS +AAA +FS +FS ACTINOBACTERIA Bifidobacteriaceae Bifidobacterium catenulatum/ N N N N N pseudocatenulatum Bifidobacterium longum N N N N Coriobacteriaceae Collinsella aerofaciens N Corynebacteriaceae Corynebacterium sp. O O O Corynebacterium aurimucosum O O Corynebacterium striatum O O BACTEROIDETES Bacteroideaceae Bacteroides caccae N Bacteroides cellulosilyticus N N Bacteroides fragilis N Bacteroides ovatus N N Bacteroides thetaiotaomicron N Bacteroides uniformis N N Bacteroides vulgatus N N N N Tannerellaceae Parabacteroides distasonis N FIRMICUTES Bacillaceae Bacillus sp. O Bacillus pumilus O O Enterococcaceae Enterococcus faecium O/N O/N O/N O O/N Enterococcus mundtii O O O Erysipelotrichaceae Clostridium innocuum N N Staphylococcaceae Staphylococcus sp. O Staphylococcus parasanguinis O PROTEOBACTERIA Enterobacteriaceae Citrobacter amalonaticus O Escherichia coli O/N O/N O/N O/N O/N EUKARYOTES Candida albicans O TOTAL N° OF DIFFERENT ISOLATES 6/9 6/9 6/7 4/7 5/3 (O/N) YCFAG: Yeast Casitone Fatty Acid Glucose medium; Δ0: medium unchanged; ΔV: medium without vitamins; ΔS: medium without short chain fatty acids; FS: fecal suspension; AAA: aromatic amino acids; SCH: Schaedler medium; O: isolated from fecal samples on corresponding medium after aerobic incubation (37 °C for 2 to 5 days); N: isolated from fecal samples on corresponding medium after anaerobic incubation (37 °C for 5 to 7 days). Table S2: Correlation between the abundance of the bacterial taxa, as assessed by means of qPCR, and estimated glomerular filtration rate (eGFR). -
Genomic Characterization of the Uncultured Bacteroidales Family S24-7 Inhabiting the Guts of Homeothermic Animals Kate L
Ormerod et al. Microbiome (2016) 4:36 DOI 10.1186/s40168-016-0181-2 RESEARCH Open Access Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals Kate L. Ormerod1, David L. A. Wood1, Nancy Lachner1, Shaan L. Gellatly2, Joshua N. Daly1, Jeremy D. Parsons3, Cristiana G. O. Dal’Molin4, Robin W. Palfreyman4, Lars K. Nielsen4, Matthew A. Cooper5, Mark Morrison6, Philip M. Hansbro2 and Philip Hugenholtz1* Abstract Background: Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeothermic animals and are increasingly being recognized as a numerically predominant member of the gut microbiota; however, little is known about the nature of their interactions with the host. Results: Here, we provide the first whole genome exploration of this family, for which we propose the name “Candidatus Homeothermaceae,” using 30 population genomes extracted from fecal samples of four different animal hosts: human, mouse, koala, and guinea pig. We infer the core metabolism of “Ca. Homeothermaceae” to be that of fermentative or nanaerobic bacteria, resembling that of related Bacteroidales families. In addition, we describe three trophic guilds within the family, plant glycan (hemicellulose and pectin), host glycan, and α-glucan, each broadly defined by increased abundance of enzymes involved in the degradation of particular carbohydrates. Conclusions: “Ca. Homeothermaceae” representatives constitute a substantial component of the murine gut microbiota, as well as being present within the human gut, and this study provides important first insights into the nature of their residency. -
Parabacteroides Distasonis
University of Groningen Parabacteroides distasonis Ezeji, Jessica C.; Sarikonda, Daven K.; Hopperton, Austin; Erkkila, Hailey L.; Cohen, Daniel E.; Martinez, Sandra P.; Cominelli, Fabio; Kuwahara, Tomomi; Dichosa, Armand E. K.; Good, Caryn E. Published in: Gut Microbes DOI: 10.1080/19490976.2021.1922241 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2021 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Ezeji, J. C., Sarikonda, D. K., Hopperton, A., Erkkila, H. L., Cohen, D. E., Martinez, S. P., Cominelli, F., Kuwahara, T., Dichosa, A. E. K., Good, C. E., Jacobs, M. R., Khoretonenko, M., Veloo, A., & Rodriguez- Palacios, A. (2021). Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. Gut Microbes, 13(1), [1922241]. https://doi.org/10.1080/19490976.2021.1922241 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. -
A Synbiotic Concept Containing Spore-Forming Bacillus Strains and A
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Ghent University Academic Bibliography International Journal of Pharmaceutics: X 1 (2019) 100021 Contents lists available at ScienceDirect International Journal of Pharmaceutics: X journal homepage: www.journals.elsevier.com/international-journal-of-pharmaceutics-x A synbiotic concept containing spore-forming Bacillus strains and a prebiotic fiber blend consistently enhanced metabolic activity by modulation of the T gut microbiome in vitro Cindy Duysburgha, Pieter Van den Abbeelea, Kiran Krishnanb, Thomas F. Bayneb, ⁎ Massimo Marzoratia,c, a ProDigest bvba, Technologiepark 82, 9052 Ghent, Belgium b Microbiome Labs, 1332 Waukegan Road, Glenview, IL 60025, USA c Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium ARTICLE INFO ABSTRACT Keywords: A standardized in vitro simulation of the human gastrointestinal tract (M-SHIME®) was used to assess the effect of Faecalibacterium prausnitzii repeated daily administration of a synbiotic formulation, containing five spore-forming Bacillus strains and a Endotoxemia prebiotic fiber blend, on the microbial activity and composition of three simulated human subjects. Firstly, while Fructooligosaccharides confirming recent findings, deeper phylogenetic insight was obtained in the resident M-SHIME® microbiota, Galactooligosaccharides demonstrating that the model maintains a diverse and representative, colon region-specific luminal and mucosal Xylooligosaccharides microbial community. Supplementation of the synbiotic concept increased microbial diversity in the distal colon Obesity areas, whereas specific enhancement of Bacillaceae levels was observed in the ascending colon suggesting a successful engraftment of the Bacillus spores, which probably resulted in a stimulatory effect on, among others, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Tannerellaceae and Faecalibacterium prausnitzii contributing directly or indirectly to stimulation of acetate, propionate and butyrate production. -
Microbial and Metabolic Relationships of the Preterm Gut Microbiome in Response to Antibiotic and Dietary Interventions
Microbial and Metabolic Relationships of the Preterm Gut Microbiome in Response to Antibiotic and Dietary Interventions by Sandi Yen A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy In Molecular and Cellular Biology Guelph, Ontario, Canada © Sandi Yen, November 2019 ABSTRACT MICROBIAL AND METABOLIC RELATIONSHIPS OF THE PRETERM GUT MICROBIOME IN RESPONSE TO ANTIBIOTIC AND DIETARY INTERVENTIONS Sandi Yen Advisors: University of Guelph, 2019 Emma Allen-Vercoe Marc G. Aucoin The progression of preterm infant gut microbiome development is intricately linked with the development of the infant, such that disruptions to the microbial system can manifest as neonatal necrotizing enterocolitis (NEC) in the infant. One of the proposed aetiologies of NEC is that disease onset occurs when microbiome development is challenged by an external perturbation, such as antibiotic treatment. The research conducted in this thesis was motivated by the overarching hypothesis that infant health occurs when homeostatic microbial relationships have been established. Conversely, when microbiome development is disrupted, the preterm infant is susceptible to diseases such as NEC. Therefore, the driving hypothesis of this thesis was that external factors, such as antibiotic therapy or formula milk, impair microbial interactions such that the preterm gut microbiome no longer sustains healthy infant development, leading to NEC onset. This hypothesis was tested using fecal microbiota from two preterm infants with different antibiotic exposures while in hospital. Propagation of these preterm fecal microbiota in an in vitro continuous culture system allowed for compositional, metabonomic, culture-based annotation of the ecosystems. Longitudinal analysis of each community revealed differences in each community’s functional capacity. -
Supplementary Table 8 Spearman's Correlations Between Targeted Urinary Urolithins and Microbiota
Supplementary material Gut Supplementary Table 8 Spearman's correlations between targeted urinary urolithins and microbiota. Urolithin- Urolithin- Urolithin- Total A- B- C- Urolithins Family level Taxonomy glucuronid glucuronid glucuronid (A+B+C) e e e Actinobacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium adolescentis_msp_0263 -0.18 -0.09 -0.16 -0.18 Bifidobacteriaceae Bifidobacterium; Bifidobacterium adolescentis Actinobacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium bifidum_msp_0419 -0.12 -0.2 -0.08 -0.13 Bifidobacteriaceae Bifidobacterium; Bifidobacterium bifidum Actinobacteria; Coriobacteriia; Coriobacteriales; Coriobacteriaceae; Collinsella; Collinsella aerofaciens_msp_1244 -0.15 -0.06 -0.04 -0.18 Coriobacteriaceae Collinsella aerofaciens Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Adlercreutzia; unclassified Adlercreutzia_msp_0396 0.09 0.01 0.16 0.12 Eggerthellaceae unclassified Adlercreutzia Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Eggerthella; Eggerthella lenta_msp_0573 0.03 -0.15 0.08 0.03 Eggerthellaceae Eggerthella lenta Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Gordonibacter; Gordonibacter urolithinfaciens_msp_1339 0.19 -0.05 0.18 0.19 Eggerthellaceae Gordonibacter urolithinfaciens Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides; Bacteroides cellulosilyticus_msp_0003 0.12 0.11 0.15 0.15 Bacteroidaceae Bacteroides cellulosilyticus Bacteroidetes; Bacteroidia; Bacteroidales; -
Bacteroidales Species Are a Reservoir of Phase-Variable Antibiotic Resistance Genes in the Human Gut Microbiome
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.26.441444; this version posted April 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Bacteroidales species are a reservoir of phase-variable antibiotic resistance genes in the human gut microbiome Wei Yana, A. Brantley Hallb,c, and Xiangfang Jianga a National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA b Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA c Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA Address correspondence to Xiaofang Jiang: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.26.441444; this version posted April 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Phase-variable antibiotic resistance genes (ARGs) can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of phase-variable ARGs remains poorly understood. Here, we sought to assess the threat posed by phase-variable ARGs by systematically searching for phase-variable ARGs in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified phase-variable ARGs and categorized them into three classes based on the invertase regulating phase variation. -
Universite D'aix-Marseille
1 2 3 UNIVERSITE D’AIX-MARSEILLE 4 Faculté de Médecine – ED 62 5 6 Institut-Hospitalo-Universitaire (IHU) – Méditerranée Infection, Marseille, 7 France / Microbes, Evolution, Phylogeny and Infection (MEΦI) - Institut de 8 Recherche pour le Développement IRD 198, Assistance Publique – Hôpitaux de 9 Marseille (AP-HM) 10 En vue d’obtenir le grade de : Docteur de l’Université d’Aix-Marseille 11 Discipline : Sciences de la Vie et de la Santé 12 Spécialité : Pathologies Humaines - Maladies Infectieuses 13 Sarah BENABDELKADER 14 Etudes microbiologiques des parodontopathies 15 Soutenue publiquement le 22 novembre 2019 devant le jury : 16 Pr. Virginie MONNET-CORTI Université Aix-Marseille Président du Jury 17 Dr Christelle POMARES Université de Nice Rapporteur 18 Pr. Raymond RUIMY Université de Nice Rapporteur 19 Dr. Gérard ABOUDHARAM Université Aix-Marseille Co-Directeur de Thèse 20 Pr Bernard LA SCOLA Université Aix-Marseille Directeur de Thèse 21 1 22 23 2 24 Remerciements 25 Je tiens à remercier mes deux encadrants, messieurs le Professeur Bernard La Scola et 26 le Docteur Gérard Aboudharam, pour leurs encadrements au cours de ces dernières années, 27 depuis le Master jusqu’à la présente Thèse. Leurs enseignements et fins conseils ont été 28 déterminants pour le déroulement de ce travail et m’ont permis de surmonter les difficultés 29 rencontrées au cours de la réalisation de ce travail. 30 Je remercie également monsieur le Professeur Didier Raoult de m’avoir accueillie au 31 sein de l’Institut Hospitalo-Universitaire, Méditerranée-Infection ; un environnement 32 scientifique particulier, stimulant l’esprit de recherche. 33 Je remercie madame le Professeur Virginie Monnet-Corti, d’avoir accepté de présider 34 au sein du jury de cette Thèse.